From 7679b19b6bb7f8fcb7ffa10e4e1e59d37870f31c Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Fri, 20 Dec 2024 14:52:37 +0100
Subject: [PATCH] Create output directories in write_*

---
 petab/v1/conditions.py   | 4 +++-
 petab/v1/core.py         | 4 +++-
 petab/v1/mapping.py      | 4 +++-
 petab/v1/measurements.py | 4 +++-
 petab/v1/observables.py  | 4 +++-
 petab/v1/parameters.py   | 4 +++-
 petab/v1/yaml.py         | 3 ++-
 petab/v2/experiments.py  | 4 +++-
 8 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/petab/v1/conditions.py b/petab/v1/conditions.py
index 4e691d62..5a856c84 100644
--- a/petab/v1/conditions.py
+++ b/petab/v1/conditions.py
@@ -60,9 +60,11 @@ def write_condition_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab condition table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_condition_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 
diff --git a/petab/v1/core.py b/petab/v1/core.py
index 10274b8c..3b4a4082 100644
--- a/petab/v1/core.py
+++ b/petab/v1/core.py
@@ -60,8 +60,10 @@ def write_simulation_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab simulation table
-        filename: Destination file name
+        filename: Destination file name. The parent directory will be created
+            if necessary.
     """
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)
 
 
diff --git a/petab/v1/mapping.py b/petab/v1/mapping.py
index bae9d5fb..7d1b25aa 100644
--- a/petab/v1/mapping.py
+++ b/petab/v1/mapping.py
@@ -60,9 +60,11 @@ def write_mapping_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab mapping table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_mapping_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 
diff --git a/petab/v1/measurements.py b/petab/v1/measurements.py
index 757ce9ce..9c730578 100644
--- a/petab/v1/measurements.py
+++ b/petab/v1/measurements.py
@@ -58,9 +58,11 @@ def write_measurement_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab measurement table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_measurement_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)
 
 
diff --git a/petab/v1/observables.py b/petab/v1/observables.py
index 1485302d..bcd0f05a 100644
--- a/petab/v1/observables.py
+++ b/petab/v1/observables.py
@@ -67,9 +67,11 @@ def write_observable_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab observable table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_observable_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 
diff --git a/petab/v1/parameters.py b/petab/v1/parameters.py
index 20457dcb..1696cc0c 100644
--- a/petab/v1/parameters.py
+++ b/petab/v1/parameters.py
@@ -112,9 +112,11 @@ def write_parameter_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab parameter table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_parameter_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 
diff --git a/petab/v1/yaml.py b/petab/v1/yaml.py
index 51159453..afb83df3 100644
--- a/petab/v1/yaml.py
+++ b/petab/v1/yaml.py
@@ -238,8 +238,9 @@ def write_yaml(yaml_config: dict[str, Any], filename: str | Path) -> None:
 
     Arguments:
         yaml_config: Data to write
-        filename: File to create
+        filename: File to create. Parent directories are created if necessary.
     """
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     with open(filename, "w") as outfile:
         yaml.dump(
             yaml_config, outfile, default_flow_style=False, sort_keys=False
diff --git a/petab/v2/experiments.py b/petab/v2/experiments.py
index 7833fa1f..def98bd7 100644
--- a/petab/v2/experiments.py
+++ b/petab/v2/experiments.py
@@ -34,7 +34,9 @@ def write_experiment_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab experiments table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_experiment_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)